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Posted to commits@taverna.apache.org by bu...@apache.org on 2015/03/09 15:20:45 UTC
svn commit: r943019 - in /websites/staging/taverna/trunk: cgi-bin/ content/
content/documentation/scufl2/workflow.html
Author: buildbot
Date: Mon Mar 9 14:20:45 2015
New Revision: 943019
Log:
Staging update by buildbot for taverna
Added:
websites/staging/taverna/trunk/content/documentation/scufl2/workflow.html
Modified:
websites/staging/taverna/trunk/cgi-bin/ (props changed)
websites/staging/taverna/trunk/content/ (props changed)
Propchange: websites/staging/taverna/trunk/cgi-bin/
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==============================================================================
--- websites/staging/taverna/trunk/content/documentation/scufl2/workflow.html (added)
+++ websites/staging/taverna/trunk/content/documentation/scufl2/workflow.html Mon Mar 9 14:20:45 2015
@@ -0,0 +1,280 @@
+<!DOCTYPE html>
+<html lang="en">
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+
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+ "@context" : "http://schema.org",
+ "@type" : ["CreativeWork"],
+ "@id": "",
+ "name" : "Scufl2-Workflow",
+ "publisher" : {
+ "@type" : "Organization",
+ "url" : "http://www.apache.org/",
+ "name" : "The Apache Software Foundation (ASF)"
+ },
+ "license": {
+ "@type": "CreativeWork",
+ "@id": "http://www.apache.org/licenses/LICENSE-2.0",
+ "url": "http://www.apache.org/licenses/LICENSE-2.0",
+ "name": "Apache License, Version 2.0"
+ }
+ }
+</script>
+
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+
+
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+
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+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="/"><img src="/img/taverna-logo-145x134.png" alt="">Apache Taverna</a>
+
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li class="dropdown">
+ <a href="/introduction" data-toggle="dropdown" role="button" aria-expanded="false">Introduction<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/introduction/taverna-features">Taverna features</a></li>
+ <li><a href="/introduction/why-use-workflows">Why use workflows?</a></li>
+ <li><a href="/introduction/what-is-in-silico-experimentation">What is âin silicoâ experimentation?</a></li>
+ <li><a href="/introduction/what-is-a-workflow-management-system">What is a Workflow Management System?</a></li>
+ <li><a href="/introduction/how-can-taverna-help-me">How can Taverna help me?</a></li>
+ <li><a href="/introduction/services-in-taverna">Services in Taverna</a></li>
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+ <li><a href="/documentation/tutorials">Tutorials</a></li>
+ <li><a href="/documentation/videos">Videos</a></li>
+ <li><a href="/documentation/example-workflows">Example workflows</a></li>
+ <li><a href="/documentation/service-sets">Service sets</a></li>
+ <li><a href="/documentation/provenance">Provenance management</a></li>
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+ <li><a href="/documentation/plugins">Plugins</a></li>
+ <li><a href="/documentation/training-and-workshops">Training and workshops</a></li>
+ <li><a href="/documentation/web-service-developers">Web service developers</a></li>
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+ <li><a href="/download/command-line-tool">Taverna Command Line</a></li>
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+ <li><a href="/download/system-requirements">System Requirements</a></li>
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+ <li><a href="/community/edit">Edit website</a></li>
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+
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+
+ <form class="navbar-form navbar-right" role="search"
+ name="search" id="search" action="http://www.google.com/search" method="get">
+ <input value="taverna.incubator.apache.org" name="sitesearch" type="hidden"/>
+ <div class="form-group input-group">
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+ </div><!--/.nav-collapse -->
+ </div><!--/.container-->
+ </nav>
+
+
+ <div id="page" class="container">
+ <h1>Scufl2-Workflow</h1>
+ <div class="alert alert-info" role="alert"><p><span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span>
+
+Taverna is transitioning to the Apache Incubator.
+This webpage reflects material not yet released under Apache Incubator.
+Instead it shows <a class="alert-link" href="http://www.taverna.org.uk/">taverna2</a> material that is expected to become part of the Apache Incubator project in the future.
+</div>
+
+
+ <div id="content"><p>The definition of a workflow, its processors, inputs/outputs and links.</p>
+<ul>
+<li>Bundle path: <code>/workflow/\$name.n3</code></li>
+</ul>
+<p>Each nested workflow (and nested nested workflows etc.) exists in a separate file within the <code>/workflow/</code> folder in the bundle.
+The bundle's <a href="/documentation/scufl2/bundle">research object</a> defines what is the top level workflow.</p>
+<h2 id="identifier">Identifier</h2>
+<p>Each workflow <strong>must</strong> have a unique name within the bundle's workflow files.
+The base part of the file name (excluding extension) <strong>must</strong> match the <strong>scufl2:name</strong> of the workflow.</p>
+<p>Workflows used in a particular research object are globally identified as
+ <code><http://ns.taverna.org.uk/2010/researchObject/$uuid/workflow/$workflowName/></code> -
+ for instance <code><http://ns.taverna.org.uk/2010/researchObject/28f7c554-4f35-401f-b34b-516e9a0ef731/workflow/Helloworld/></code>.</p>
+<p>As it can be useful to identify nested workflows included in several workflow bundles,
+ each workflow must also have a <em>scufl2:workflowIdentifier</em> property, which URI <strong>must</strong> be on the form
+ <code><http://ns.taverna.org.uk/2010/workflow/$uuid></code>, for example
+ <code><http://ns.taverna.org.uk/2010/workflow/efb1cdcd-1e19-408a-885a-303c6553a672/></code>.
+It is responsibility of the software creating or modifying the workflow to generate a new workflowcIdentifier
+ as soon as the workflow has changed.
+(The randomly generated UUID of the workflow must <strong>not</strong> match the UUID of a research object or any other workflow.)
+The owning <a href="/documentation/scufl2/bundle">research object</a> should then also be assigned a new UUID.
+(Note that editing metadata and bindings in other files don't update the workflow, but still update the research object.)</p>
+<p>The workflow file <strong>should</strong> set the @base to the form <code><workflow/$name></code>}
+ so that nested resources can be referenced relatively, like {{<processor/$processorName></code>.</p></p>
+<h2 id="example">Example</h2>
+<p>(Outdated)</p>
+<div class="codehilite"><pre><span class="p">@</span><span class="n">base</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">workflow</span><span class="o">/</span><span class="n">Helloworld</span><span class="o">/&</span><span class="n">gt</span><span class="p">;</span>
+<span class="p">@</span><span class="n">prefix</span> <span class="n">scufl2</span><span class="p">:</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">ns</span><span class="p">.</span><span class="n">taverna</span><span class="p">.</span><span class="n">org</span><span class="p">.</span><span class="n">uk</span><span class="o">/</span>2010<span class="o">/</span><span class="n">scufl2</span><span class="o">/</span><span class="n">ontology</span><span class="o">/&</span><span class="n">gt</span><span class="p">;</span> <span class="p">.</span>
+
+<span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="o">&</span><span class="n">gt</span><span class="p">;</span>
+ <span class="n">a</span> <span class="n">scufl2</span><span class="p">:</span><span class="n">Workflow</span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span class="n">name</span> <span class="o">&</span><span class="n">quot</span><span class="p">;</span><span class="n">Helloworld</span><span class="o">&</span><span class="n">quot</span><span class="p">;</span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span class="n">inputWorkflowPort</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">in</span><span class="o">/</span><span class="n">yourName</span><span class="o">&</span><span class="n">gt</span><span class="p">;</span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span class="n">outputWorkflowPort</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">out</span><span class="o">/</span><span class="n">results</span><span class="o">&</span><span class="n">gt</span><span class="p">;</span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span class="n">datalink</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">datalink</span><span class="o">/</span>1<span class="o">&</span><span class="n">gt</span><span class="p">;,</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">datalink</span><span class="o">/</span>2<span class="o">&</span><span class="n">gt</span><span class="p">;</span> <span class="p">;</span>
+ <span class="n">scufl2</span><span class="p">:</span><span class="n">processor</span> <span class="o">&</span><span class="n">lt</span><span class="p">;</span><span class="n">processor</span><span class="o">/</span><span class="n">Hello</span><span class="o">&</span><span class="n">gt</span><span class="p">;</span> <span class="p">.</span>
+<span class="p">]]</span><span class="o">></span>
+</pre></div>
+
+
+<p>This example defines the workflow "HelloWorld".
+It contains one workflow input port and one workflow output port, in addition to a single processor and two datalinks.</p>
+<p>The nested resources for this workflow, such as InputWorkflowPort , OutputWorkflowPort,
+ <a href="/documentation/scufl2/datalink">DataLink</a>, Processor and their children <strong>should</strong> be described
+ in the same file as the workflow itself.
+Additional metadata should be added to an <code>/annotations/</code> file.</p>
+<h2 id="properties">Properties</h2>
+<ul>
+<li><strong>scufl2:name</strong> (required) gives the programmatic short-name for this workflow within this bundle.
+ This must be unique among the other workflows.</li>
+<li><strong>scufl2:workflowIdentifier</strong> (required) gives the globally unique URI defining this workflow.
+ See <em>Identifier</em> above.</li>
+<li><strong>scufl2:inputWorkflowPort</strong> (optional) All workflow input ports defined for this workflow.</li>
+<li><strong>scufl2:outputWorkflowPort</strong> (optional) All workflow output ports defined for this workflow.</li>
+<li><strong>scufl2:datalink</strong> (optional) All <a href="/documentation/scufl2/datalink">datalinks</a>
+ defined between workflow and processor ports in this workflow.
+ (Note that if this is a nested workflow, its outside links are defined in the parent workflow)</li>
+<li><strong>scufl2:processor</strong> (optional) All <a href="/documentation/scufl2/processors">processors</a> in this workflow.</li>
+</ul>
+<h2 id="bundle-links">Bundle links</h2>
+<p>All nested workflow resources should also be defined in the same archive file as this workflow.
+Their URIs <strong>must</strong> be relative to this workflow, their type and <strong>scufl2:name</strong>.
+So for instance <workflow/Helloworld/processor/Hello> is a <strong>scufl2:Processor</strong> in <workflow/Helloworld>,
+ and has a <strong>scufl2:name</strong> "Hello".</p></div>
+
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